[Bioc-devel] Candidates for BiocGenerics

[Hervé Pagès]

On 03/01/2012 10:55 AM, Martin Morgan wrote:
> On 03/01/2012 10:20 AM, Hervé Pagès wrote:
>> Hi Benilton, Sean,
>>
>> On 03/01/2012 08:18 AM, Sean Davis wrote:
>>> On Thu, Mar 1, 2012 at 7:57 AM, Benilton Carvalho
>>> <beniltoncarvalho at gmail.com> wrote:
>>>> Hi,
>>>>
>>>> I'm implementing a few things in oligo and I wonder if it'd make
>>>> sense to have
>>>>
>>>> boxplot/coef/image/ncol/residuals
>>>>
>>>> defined in BiocGenerics?
>>>>
>>>> If it's only me using them, I'm happy to have everything in oligo.
>>>>
>>>> Thoughts?
>>>
>>> It seems that if someone is proposing a generic for functionality
>>> already in base R, that generic is by definition a good candidate for
>>> inclusion in BiocGenerics.
>>
>> I agree.
>>
>>> Are there downsides to having this be a
>>> criterion for inclusion?
>>
>> Not that I know of.
>>
>> I'll add boxplot, coef, image, ncol and residuals to BiocGenerics today.
>> I'll also add nrow, NROW, NCOL and dim, which are all interconnected
>> with ncol.
>
> I had not really been aware that 'stats4' plays the same kind of role,
> in a limited sense, in base R. So for these
>
>  > grep("^[^.]", getNamespaceExports("stats4"), value=TRUE)
> [1] "AIC" "BIC" "coef" "confint" "logLik" "mle" "nobs"
> [8] "plot" "profile" "show" "summary" "update" "vcov"
>
> one would like instead to Imports: stats and importFrom(stats, plot)
> etc. This means that recent changes to add plot and summary to
> BiocGenerics should be undone...

Arghh... good catch! OK, I'll remove plot and summary from BiocGenerics.
That also means that I don't need to add coef there.

H.

>
> Martin
>
>  >
>
>>
>> Cheers,
>> H.
>>
>>>
>>> Sean
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>
>


-- 
Hervé Pagès

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